• Journal of Microbiology and Biotechnology
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• 제14권6호
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• pp.1286-1294
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• 2004

In a previous study by the current authors, hepatocellular carcinoma (HCC) was determined to be epidemiologically sex-dependent, and the incidence and multiplicity of HCC found to decrease in estradiol-3 benzoate (EB)-treated F344 rats. Therefore, to ascertain the anticancer mechanism of EB, a commercially available cDNA microarray, with a total of 14,815 cDNA rat gene clones, was used to determine the differentially expressed genes in nontreated livers, EB-treated livers, and diethynitrosolamine (DEN)-induced HCC. In the sequenced experiment, a total of 85 genes were differentially expressed at either two or more times the rate of the normal expression, where 33 genes were downregulated by EB, and 52 genes upregulated. Candidate genes were selected according to significant changes observed in the mRNA expression in the EB-treated livers compared with the nontreated livers, then these genes were filtered according to their different expression patterns in the DEN-induced tumors compared to the estrogen-treated livers. To confirm the microarray data, a real-time PCR analysis was performed for ten selected genes: the H-ras revertant protein 107 (H­rev107), insulin-like growth factor binding protein (lOFBP), parathyroid hormone receptor (PI'HR), SH3 domain binding protein (SH3BP), metallothionein, src-suppressed C-kinase substrate (SSeCK) gene, phosphodiesterase I, CD44, epithelial membrane protein 3 (EMP3), and estrogen receptor a (ERa). The SSeCK and phosphodiesterase I genes were both upregulated in the DEN-induced hepatocarcinomas, yet their possible carcinogenic functions remain unknown. Meanwhile, the other genes were downregulated, including the genes related to growth regulation (IOFBP, H-revI07, ER$\alpha$), adipogenesis inhibition (PTHR), and tumor suppression (metallothionein).

• Journal of Microbiology and Biotechnology
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• 제15권6호
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• pp.1240-1249
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• 2005

Saccharomyces cerevisiae KNU5377 has potential as an industrial strain that can ferment wasted paper for fuel ethanol at $40^{\circ}C$ [15, 16]. To understand the characteristics of the strain, genome-wide expression was performed using DNA microarray technology. We compared the homology of the DNA microarray between genomic DNAs of S. cerevisiae KNU5377 and a control strain, S. cerevisiae S288C. Approximately $97\%$ of the genes in S. cerevisiae KNU5377 were identified with those of the reference strain. YHR053c (CUP1), YLR155c (ASP3), and YDR038c (ENA5) showed lower homology than those of S. cerevisiae S288C. In particular, the differences in the regions of YHR053c and YLR155c were confirmed by Southern hybridization, but did not with that of the region of YDR038c. The expression level of mRNA in S. cerevisiae KNU5377 and S288C was also compared: the 550 ORFs of S. cerevisiae KNU5377 showed more than two-fold higher intensity than those of S. cerevisiae S288C. Among the 550 ORFs, 59 ORFs belonged to the groups of ribosomal proteins and mitochondrial ribosomal proteins, and 200 ORFs belonged to the group of cellular organization. DIP5 and GAP1 were the most highly expressed genes. These results suggest that upregulated DIP5 and GAP 1 might take the place of ASP3 and, additionally, the sensitivity against copper might be contributable to the lowest expression level of copper-binding metallothioneins encoded by CUP 1a (YHR053c) and CUP1b (YHR055c) in S. cerevisiae KNU5377.

• 대한의생명과학회지
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• 제15권1호
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• pp.97-99
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• 2009

Geldanamycin is a benzoquinone ansamycin antibiotic that binds to cytosol HSP90 (Heat Shock Protein 90) and changes its biological function. HSP90 is involved in the intracellular important roles for the regulation of the cell cycle, cell growth, cell survival, apoptosis, angiogenesis and oncogenesis. To identify genes expressed during geldanamycin treatment against neurons of rats (PC12 cells), DNA microarray method was used. We have isolated 2 gene groups (up-or down-regulated genes) which are geldanamycin differentially expressed in neurons. Granzyme B is the gene most significantly increased among 204 up-regulated genes (more than 2 fold over-expression) and Chemokine (C-C motif) ligand 20 is the gene most dramatically decreased among 491 down-regulated genes (more than 2 fold down-expression). The gene increased expression of Cxc110, Cyp11a1, Gadd45a, Gja1, Gpx2, Ifua4, Inpp5e, Sox4, and Stip1 are involved stress-response gene, and Cryab, Dnaja1, Hspa1a, Hspa8, Hspca, Hspcb, Hspd1, Hspd1, and Hsph1 are strongly associated with protein folding. Cell cycle associated genes (Bc13, Brca2, Ccnf, Cdk2, Ddit3, Dusp6, E2f1, Illa, and Junb) and inflammatory response associated genes (Cc12, Cc120, Cxc12, Il23a, Nos2, Nppb, Tgfb1, Tlr2, and Tnt) are down-regulated more than 2 times by geldanamycin treatment. We found that geldanamycin is related to expression of many genes associated with stress response, protein folding, cell cycle, and inflammation by DNA microarray analysis. Further experimental molecular studies will be needed to figure out the exact biological function of various genes described above and the physiological change of neuronal cells by geldanamycin. The resulting data will give the one of the good clues for understanding of geldanamycin under molecular level in the neurons.

• Molecules and Cells
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• 제26권4호
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• pp.338-343
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• 2008

An embryonic stem cell is a powerful tool for investigation of early development in vitro. The study of embryonic stem cell mediated neuronal differentiation allows for improved understanding of the mechanisms involved in embryonic neuronal development. We investigated expression profile changes using time course cDNA microarray to identify clues for the signaling network of neuronal differentiation. For the short time course microarray data, pattern analysis based on the quadratic regression method is an effective approach for identification and classification of a variety of expressed genes that have biological relevance. We studied the expression patterns, at each of 5 stages, after neuronal induction at the mRNA level of embryonic stem cells using the quadratic regression method for pattern analysis. As a result, a total of 316 genes (3.1%) including 166 (1.7%) informative genes in 8 possible expression patterns were identified by pattern analysis. Among the selected genes associated with neurological system, all three genes showing linearly increasing pattern over time, and one gene showing decreasing pattern over time, were verified by RT-PCR. Therefore, an increase in gene expression over time, in a linear pattern, may be associated with embryonic development. The genes: Tcfap2c, Ttr, Wnt3a, Btg2 and Foxk1 detected by pattern analysis, and verified by RT-PCR simultaneously, may be candidate markers associated with the development of the nervous system. Our study shows that pattern analysis, using the quadratic regression method, is very useful for investigation of time course cDNA microarray data. The pattern analysis used in this study has biological significance for the study of embryonic stem cells.

• BMB Reports
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• 제40권5호
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• pp.814-824
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• 2007

Liver cirrhosis (LC) is defined as comprising diffuse fibrosis and regenerating nodules of the liver. The biochemical and anatomical dysfunction in LC results from both reduced liver cell number and portal vascular derangement. Although several studies have investigated dysregulated genes in cirrhotic nodules, little is known about the genes implicated in the pathophysiologic change of LC or about their relationship with the degree of decompensation. Here, we applied cDNA microarray analysis using 38 HBsAg-positive LC specimens to identify the genes dysregulated in HBV-associated LC and to evaluate their relation to disease severity. Among 1063 known cancer- and apoptosis-related genes, we identified 104 genes that were significantly up- (44) or down- (60) regulated in LC. Interestingly, this subset of 104 genes was characteristically correlated with the degree of decompensation, called the Pugh-Child classification (20 Pugh-Child A, 10 Pugh-Child B, and 8 Pugh-Child C). Patient samples from Pugh-Child C exhibited a distinct pattern of gene expression relative to those of Pugh-Child A and B. Especially in Pugh-Child C, genes encoding hepatic proteins and metabolizing enzymes were significantly down-regulated, while genes encoding various molecules related to cell replication were up-regulated. Our results suggest that subsets of genes in liver cells correspond to the pathophysiologic change of LC according to disease severity and possibly to hepatocarcinogenesis.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.74-82
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• 2000

Prostate cancer initially responds and regresses in response to androgen depletion therapy, but most human prostate cancers will eventually recur, and re-grow as an androgen independent tumor. Once these tumors become hormone refractory, they usually are incurable leading to death for the patient. Little is known about the molecular details of how prostate cancer cells regress following androgen ablation and which genes are involved in the androgen independent growth following the development of resistance to therapy. Such knowledge would reveal putative drug targets useful in the rational therapeutic design to prevent therapy resistance and control androgen independent growth. The application of genome scale technologies have permitted new insights into the molecular mechanisms associated with these processes. Specifically, we have applied functional genomics using high density cDNA microarray analysis for parallel gene expression analysis of prostate cancer in an experimental xenograft system during androgen withdrawal therapy, and following therapy resistance, The large amount of expression data generated posed a formidable bioinformatics challenge. A novel template based gene clustering algorithm was developed and applied to the data to discover the genes that respond to androgen ablation. The data show restoration of expression of androgen dependent genes in the recurrent tumors and other signaling genes. Together, the discovered genes appear to be involved in prostate cancer cell growth and therapy resistance in this system. We have also developed and applied tissue microarray (TMA) technology for high throughput molecular analysis of hundreds to thousands of clinical specimens simultaneously. TMA analysis was used for rapid clinical translation of candidate genes discovered by cDNA microarray analysis to determine their clinical utility as diagnostic, prognostic, and therapeutic targets. Finally, we have developed a bioinformatic approach to combine pharmacogenomic data on the efficacy and specificity of various drugs to target the discovered prostate cancer growth associated candidate genes in an attempt to improve current therapeutics.

• Asian-Australasian Journal of Animal Sciences
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• 제18권8호
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• pp.1080-1087
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• 2005

By screening specific genes related to the muscle growth of swine using cDNA microarray technology, a total of 5 novel genes (GF (growth factor) I, II, III, IV and V) were identified. Results of southern blotting to investigate the number of copies of these genes in the genome of swine indicated that GF I, GF III, and GF V existed as one copy and GF II, and GF IV existed as more than two copies. It was suggested that there are many isoforms of these genes in the genome of swine. Also, results of northern blotting to investigate whether these genes were expressed in grown muscle, using GF I, III, and V indicated that all the genes were much more expressed in the muscle of swine with body weight of 90 kg. Expression patterns of these genes in other organs, namely muscle and propagation and fat tissues, were investigated by extracting RNA from the tissues. These genes were not expressed in the propagation and fat tissues, but were expressed in the muscle tissue. To determine the mechanism of muscle growth, further studies should be preceded using the 3 specific genes related to muscle growth, that is GF I, III, and V.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2004년도 봄 학술발표논문집 Vol.31 No.1 (B)
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• pp.247-249
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• 2004

마이크로어레이 기술은 근래에 개발된 신기술로써 동시에 수천-수만 개의 유전자 발현을 측정할 수 있어 다양한 생물학적 연구에 이용되고 있다. 여러 단계의 실험 과정과 이를 통해 얻은 다량의 데이터를 처리하기 위해서는 이를 효율적으로 관리. 저장, 분석할 수 있는 통할 정보 관리 시스템을 필요로 한다. 현재 외국에서는 몇몇 관리시스템이 개발되어 있고. 국내에서도 WEMA 등이 있지만 아직 데이터 관리부분에 기능이 치우쳐 있다. 따라서 우리는 복잡한 자료구조를 가지는 마이크로어레이의 실험 정보와 각 단계별 처리 정보 등을 사용자의 관점에서 효과적이고 체계적으로 관리할 수 있고, 데이터 정규화 및 다양한 통계적 분석 기능을 갖춰 불필요한 시간과 비용을 줄임으로써 마이크로어레이 연구에 도움을 주고자 통합 분석관리 시스템 cMAMS (cDNA Microarray Analysis and Management System)를 개발하였다. 웹 기반으로 구현된 cMAMS는 데이터를 저장, 관리하는 부분과 데이터를 분석하는 부분, 그리고 모든 관련 점보가 저장되는 데이터베이스 부분으로 구성되어 있다 데이터관리부분에서는 WEMA의 계층적 데이터구조론 도입해 관리의 효율성을 높이고 시스템의 이용자를 시스템운영자, 프로젝트관리자, 일반사용자로 구분하여 데이터 접근을 제한함으로써 보안성을 높였다. 통계처리 언어 R로 구현된 데이터분석 부분은 7 단계의 다양한 분석(전처리 정규화, 가시화, 군집분석. 판별분석, 특이적 발현 유전자 선뿐, 마이크로어레이 간의 상판분석)이 가능하도록 구현하였고, 분석결과는 데이터베이스에 저장되어 추후에 검토 및 연구자간의 공유가 가능하도록 하였다. 데이터베이스는 실험정보가 저장된 데이터베이스, 분석결과가 저장된 데이터베이스, 그리고 유전자 정보 탐색을 위한 데이터베이스로 분류해 데이터를 효율적으로 관리할 수 있게 하였다. 본 시스템은 LiNUX를 운영체계로 하고 데이터베이스는 MYSQL로 하여 JSP, Perl. 통계처리 언어인 R로 구현되었다.

• Asian Pacific Journal of Cancer Prevention
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• 제13권9호
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• pp.4793-4799
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• 2012

Hypoxia is commonly featured during glioma growth and plays an important role in the processes underlying tumor progression to increasing malignancy. Here we compared the gene expression profiles of rat C6 malignant glioma cells under normoxic and hypoxic conditions by cDNA microarray analysis. Compared to normoxic culture conditions, 180 genes were up-regulated and 67 genes were down-regulated under hypoxia mimicked by $CoCl_2$ treatment. These differentially expressed genes were involved in mutiple biological functions including development and differentiation, immune and stress response, metabolic process, and cellular physiological response. It was found that hypoxia significantly regulated genes involved in regulation of glycolysis and cell differentiation, as well as intracellular signalling pathways related to Notch and focal adhesion, which are closely associated with tumor malignant growth. These results should facilitate investigation of the role of hypoxia in the glioma development and exploration of therapeutic targets for inhibition of glioma growth.

• Journal of Applied Biological Chemistry
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• 제55권4호
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• pp.227-234
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• 2012

유채 종자 성숙단계별 변화하는 종자의 특성을 살펴본 결과, 개화 후 25일된 미성숙 종자에서 지방산 생성이 관찰되기 시작하였으며, 개화 후 35일된 미성숙 종자에서 지방산 생성이 거의 최고치에 달하는 것을 관찰하였으며, 이 때 백립중이 406 mg으로 가장 무거웠다. 유채 300k Microarray를 이용하여 유채 종자 성숙단계별 발현되는 유전자의 발현양상을 살펴보았다. 유채 300k Microarray는 NCBI에 등록되어 있는 543,448개의 ESTs와 780개의 cDNA정보를 군집 분석하여 80,696개의 유전자정보를 얻어 제작되었다. 개화 후 10, 25, 그리고 35일된 종자에서 total RNA를 분리하여 유채 300k Microarray 실험을 수행한 결과, 약 7,000개의 유전자에 해당하는 8.5%가 잎에 비해 종자(25DAF)에서 발현 양이 2배 이상 증가됨을 알 수 있었고, 10배 이상 증가하는 유전자 비율도 0.4%에 해당하였다. 종자 특이 발현 유전자의 발현양상을 보면, 초기에는 저장 및 세포분화 관련 유전자들의 발현 양이 높게 나타난 반면, 후기에는 지방산 대사 관련 유전자를 포함한 에너지 축적 관련 유전자들의 발현 양이 높게 나타나는 것을 관찰 할 수 있었으며, reverse transcriptase-polymerase chain reaction을 통해서 이를 확인하였다. 본 실험 결과는 종자 특이 발현 프로모터를 발굴하거나 특정 대사 기작 연구에 관여하는 유전자 발현 양상을 광범위하게 살펴봄으로써 좀 더 심도 있는 연구를 할 수 있는 기초자료를 제공하는데 많은 도움이 될 거라 사료된다.